It depends what the stones are made of. I have been doing cleanses for 2 years, did GCG etc, chanca piedra, fosfood etc. Doing now lemonjuice, peppermintoil capsules and chammomil. I am pretty well clean except for one calcified stone they said it was 2.8cm, last time 2.4cm, but I wonder how precise their measurements are. One person did the GCG for a year but it only shrunk a couple of mm and decided to go for surgery.
It is up to you but I would flush.